Can a court with lack of subject matter jurisdiction permit trumped-up criminal charges and indigent defendant to stand trial on charges not made in indictment?

Can a court with lack of subject matter jurisdiction permit indigent defendant to stand trial without his alleged accuser of rape who disappeared without a trace and refused to testify in court?

Can a United States Magistrate Judge with lack of subject matter jurisdiction be allowed to issue a Report and Recommendation on a writ of habeas corpus to a district judge?

Can a court with lack of subject matter jurisdiction permit an indigent defendant to stand trial on trumped-up criminal charges not made in indictment?